Contacts of the helix formed by residues 110 - 120 (chain C) in PDB entry 3P05
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 110 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C SER* 1.3 74.5 - - - +
111C LEU* 1.3 64.8 + - - +
112C GLN* 3.3 17.2 + - - +
113C GLU* 2.9 40.7 + - - +
114C GLN* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C HIS* 3.6 39.9 - - + +
48C THR* 4.2 8.3 - - + +
50C GLN* 3.8 34.1 - - - +
109C SER 4.1 0.6 + - - -
110C THR* 1.3 71.7 - - - +
112C GLN* 1.3 75.3 + - - +
114C GLN* 3.2 20.8 + - - +
115C ILE* 3.0 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C MET* 5.2 0.2 - - - +
110C THR* 3.0 18.0 - - - +
111C LEU* 1.3 97.9 + - + +
113C GLU* 1.3 62.4 + - - +
115C ILE* 3.9 8.7 - - + +
116C GLY* 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C MET* 3.7 19.7 - - + +
97C ARG* 2.8 44.6 + - - +
108C THR 4.4 0.7 - - - +
109C SER* 3.5 1.9 - - - -
110C THR* 2.9 48.5 + - - +
112C GLN* 1.3 75.4 - - - +
114C GLN* 1.3 64.6 + - - +
116C GLY* 3.2 1.2 + - - -
117C TRP* 2.9 44.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C THR* 3.7 10.3 - - - -
49C PRO* 3.4 31.0 - - + +
50C GLN* 3.2 30.7 + - - +
103C ASP 4.6 0.9 - - - +
106C GLY* 3.8 15.8 + - - -
109C SER* 3.0 38.6 + - - +
110C THR 2.9 17.6 + - - +
111C LEU* 3.6 10.6 - - - +
113C GLU* 1.3 74.8 - - - +
115C ILE* 1.3 63.4 + - - +
117C TRP* 3.4 12.4 + - + +
118C MET* 3.1 31.6 + - - +
126C VAL* 4.0 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ILE* 4.1 20.6 - - + -
12C HIS* 3.6 38.4 - - + +
48C THR* 4.7 1.6 - - + -
111C LEU* 3.0 32.8 + - + +
112C GLN* 3.9 8.7 - - + +
114C GLN* 1.3 74.1 - - - +
116C GLY* 1.3 61.0 + - - +
118C MET 3.2 0.2 + - - -
119C THR* 2.7 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C MET* 3.8 17.7 - - - +
112C GLN 2.9 15.6 + - - -
113C GLU 3.2 4.5 + - - -
115C ILE* 1.3 76.8 - - - +
117C TRP* 1.3 56.7 + - - +
119C THR* 3.8 3.4 + - - -
120C HIS* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C MET* 3.6 25.3 - - + +
97C ARG* 2.8 53.5 + - + -
99C PRO* 3.8 23.9 - - + +
103C ASP* 3.8 28.5 - - + -
109C SER* 3.8 15.9 - - - -
113C GLU* 2.9 42.1 + - + +
114C GLN* 3.8 10.3 - - + +
116C GLY* 1.3 75.2 - - - +
118C MET* 1.3 62.2 + - - +
119C THR 3.5 0.2 + - - -
120C HIS* 3.6 10.5 - + + +
124C ILE* 2.7 60.9 + - + +
126C VAL* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ILE* 3.9 22.2 - - + -
46C GLY* 3.9 16.6 - - - +
47C ALA 3.5 22.7 - - - +
48C THR* 4.0 20.4 - - - -
49C PRO* 4.2 1.1 - - - -
114C GLN 3.1 20.5 + - - +
115C ILE 3.2 2.9 + - - +
117C TRP* 1.3 76.9 - - - +
119C THR* 1.3 60.1 + - + +
120C HIS 3.5 0.2 - - - -
123C PRO* 3.4 18.1 - - - +
124C ILE 3.6 5.6 - - - +
125C PRO* 4.5 4.9 - - + +
126C VAL* 3.6 33.0 - - + +
127C GLY* 3.9 9.4 - - - +
128C GLU* 5.5 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ILE* 4.1 31.6 - - + -
10C MET* 5.7 5.8 - - + +
115C ILE* 2.7 32.7 + - + +
116C GLY* 3.8 3.3 + - - -
118C MET* 1.3 79.2 - - - +
120C HIS* 1.3 69.4 + - - +
121C ASN* 3.7 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C MET* 5.0 21.7 + - + -
116C GLY 2.9 18.0 + - - +
117C TRP* 3.6 14.8 - + - +
118C MET 3.5 0.2 - - - -
119C THR* 1.3 85.2 - - - +
121C ASN* 1.3 77.9 + - - +
122C PRO* 2.7 29.9 + - + +
123C PRO* 3.1 21.1 - - - +
124C ILE* 4.8 9.2 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il